You guys have always the strangest problems!
Can't you have simple questions only?
Well, I suppose it's the case at fault if the drive is still working. the data shouldn't have changed but you could always check the iso integrity with WiiBackupManager (Sha1 option to verify the iso).
changing the HDD case shouldn't affect the gameplay (like, not receiving Wiimote or reset informations).
Freeze and no music could be caused by a sleep mode of the drive controlled by the case I guess (but in my opinion it should be set by the HDD itself not the USB2IDE adapter).
Your USB cable has any specific device included or it's a simple USB to USB wire?
I can't help you more than that, I don't know hardware good enough to understand how things work and which element is responsible to your problem.
@[member='JordenNixNix']:
your VC channels are on real NAND or emulated NAND?
Ocarina doesn't work on Emulated NAND (at least, I could never make it work on the games I tested it).
So you need to launch the channel from the real NAND.
Launching channels have two different method:
Content or
boot.dol
If ocarina doesn't work, try changing the boot method in the settings > loader settings > Channel boot method.